I have a Thule rack on my E46 and it works great for carrying the bikes. With the hard-points in the roof, it is very solid and there's no chance for marking your roof unless you slip when installing or removing it.

the e60 does not have the screw points of previous model BMW's...inside the door jam there is a little indentation that the rack grabs onto and it also grabs on the rain gutter. The BMW racks are made by Saris and are very high quality...better than Yakima and Thule IMO and the price is no higher if you get it at a discount. Crevier BMW in California has an internet parts department and their prices are pretty good.